Just bought a Yakima cargo box for our wagon. Using it with the Yakima rack I used for bikes. Same as the Thule racks. I am wondering if I could just mount the box on the factory cross bars and not use the Yakima rack. It would reduce the overall height by about four inches or so, probably reduce some of the wind noise too.
I have heard that the factory rack and cross bars are only rated for skis and not much more. Has anyone had experience with this? Thanks.

According to the manual for my '89 TE, you can load up to 220 lbs when using a M-B approved roof rack. The roof itself can support up to 175 lbs. The crossbars are only referred to as luggage retainers and appear to have no other function.

The problem you'll run into is with the fact that the factory crossbars are curved, whereas the bottom of your cargo box is not. I suppose you could shim it, but then the box would only contact your crossbars at those shim points, not the entire bar's length as was likely intended by the box's designers.

I use my Thule crossbars exclusively when I install my cargo box...that's my 2% of a buck

I am not familiar with the Yamike cargo box, but when I bought my E320T the dealer gave me a catalog of all the original M.B. cargo boxes and sets you can fit to the rails at the roof of the T-series.

Believe me, skies are just one of the hundreds of things Mercedes design the racks to hold. There are a ton of different aerodinamic cargo boxes that attach directly into the rails (they vary in sizes and prices). There are racks for skies (as mentioned) but also for bikes, surf boards, camping equipment and tents, model airplanes, sky gliders, canoes, boats (of all types and sizes), field equipment for surveyors, well, almost everything but the kitchen sink.

All of them are listed as original Mercedes-Benz accessories and some can be even ordered to match your car's color.